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Old 10-10-2017, 05:11 PM   #108
ashuchawla
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Location: san diego

Join Date: Jan 2012
Posts: 38
Default Confusion regarding read merging

Dear Brian, or anybody else who could help me,

I used the following command for BBMerge:
bbmerge.sh in=reads.fq out=merged.fq pfilter=1

I got theses stats:
Pairs: 2545201
Joined: 1491688 58.61%
Ambiguous: 439613 17.27%
No Solution: 613393 24.10%
Too Short: 0 0.00%
Avg Insert: 322.6

My questions:
1. What happens to the bases while read merging if there is a mismatch outside of the 12 bases this command considers. As per my understanding, Minimum number of overlapping bases to allow merging is 12. In other words, could you please explain exactly how does the merge happen between two paired end reads when I use the above mentioned command for a perfect overlap?

2. Could you please explain, what do "Ambiguous" and "No solution" mean?

Thank you so much,
Ashu
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